This repository contains Jupyter notebooks, Python scripts and a module (in OISST.py) to calculate, map and plot a series of diagnostics related to Sea Surface Temperature (SST) anomalies and Marine Heat Wave (MHW) conditions around Aotearoa New Zealand.
Author: Nicolas Fauchereau
The first port of call is the scripts directory.
It contains 4 scripts:
update the OISST dataset locally for a given geographical domain
Plots the maps of SST anomalies with MHW conditions stippled, and the maps showing the number of consecutive periods (1, 7, 30 days) to date with MHW conditions
Plots the time-series of the Aotearoa New Zealand 6 coastal SST indices (see figures below)
Plots the time-series of the Ninos indices ('1+2', '3', '4', '3.4', 'ONI')
Below is the help for these scripts
usage: update_OISST.py [-h] [-y YEAR] [-o OPATH] [-d DOMAIN] [-t TRYDAP]
Download the yearly OISST v2 netcdfs from the PSL
optional arguments:
-h, --help show this help message and exit
-y YEAR, --year YEAR The year to download the OISST v2 netcdf file for Note: - root URL is
https://downloads.psl.noaa.gov/Datasets/noaa.oisst.v2.highres/ - The filename pattern is sst.day.mean.${year}.v2.nc
-o OPATH, --opath OPATH
The root path where to download the OISST datasets, default to '/media/nicolasf/END19101/data/OISST/daily/'
-d DOMAIN, --domain DOMAIN
the domain for which to download / extract, can be in ['NZ','Ninos','IOD'], default to 'NZ'
-t TRYDAP, --tryDAP TRYDAP
Whether to try the PSL DAP server, probably better to leave it at 0 (default, which means False)
Always check data availability at https://downloads.psl.noaa.gov/Datasets/noaa.oisst.v2.highres/
usage: OISST_realtime_NZ_maps.py [-h] [-l LAG] [-q QUANTILE] [-d DOMAIN] [-i IPATH] [-c CLIM_PATH] [-f FIG_PATH] [-n NDAYS_AGG] [-b NDAYS_BACK]
Maps the SST anomalies around NZ along with the MHWs conditions
optional arguments:
-h, --help show this help message and exit
-l LAG, --lag LAG lag (in days) WRT to realtime, default 0
-q QUANTILE, --quantile QUANTILE
The quantile threshold used to define heatwave conditions, default 0.9 (90th percentile)
-d DOMAIN, --domain DOMAIN
The domain for which to download / extract, can be in ['NZ','Ninos','IOD'], default to 'NZ'
-i IPATH, --ipath IPATH
The root path where the downloaded OISST datasets are, default to '/media/nicolasf/END19101/data/OISST/daily'
-c CLIM_PATH, --clim_path CLIM_PATH
The path to the zarr files containing the percentile climatologies, default to
'/home/nicolasf/operational/OISST_indices/outputs/'
-f FIG_PATH, --fig_path FIG_PATH
The path to where the figures are saved, default to '/home/nicolasf/operational/OISST_indices/figures/'
-n NDAYS_AGG, --ndays_agg NDAYS_AGG
The averaging period in days, can be in [1, 7, 30] currently
-b NDAYS_BACK, --ndays_back NDAYS_BACK
The number of days to look back for the calculation of the cumulative MHWs conditions, default 10 years (3650 days)
Relies on `update_OISST.py` to be run first
usage: OISST_realtime_NZ_indices.py [-h] [-d DOMAIN] [-i IPATH] [-c CLIM_PATH] [-s SHAPES_PATH] [-f FIG_PATH] [-o CSV_PATH] [-n NDAYS_AGG] [-m NMONTHS_BACK]
Plot the time-series of OISST V2 SST anomalies for the 6 NZ coastal regions
optional arguments:
-h, --help show this help message and exit
-d DOMAIN, --domain DOMAIN
The domain for which to download / extract, can be in ['NZ','Ninos','IOD'], default to 'NZ' and should not change ...
-i IPATH, --ipath IPATH
The root path where the downloaded OISST datasets are, default to '/media/nicolasf/END19101/data/OISST/daily'
-c CLIM_PATH, --clim_path CLIM_PATH
The path to the zarr files containing the climatologies, default to '/home/nicolasf/operational/OISST_indices/outputs/'
-s SHAPES_PATH, --shapes_path SHAPES_PATH
The path to the shapefiles used to delineates the 6 NZ coastal regions, default to '/home/nicolasf/operational/OISST_indices/data/shapefiles/'
-f FIG_PATH, --fig_path FIG_PATH
The path to where the figures are saved, default to '/home/nicolasf/operational/OISST_indices/figures/'
-o CSV_PATH, --csv_path CSV_PATH
The path to where the csv files containing the time-series are saved '/home/nicolasf/operational/OISST_indices/outputs/'
-n NDAYS_AGG, --ndays_agg NDAYS_AGG
The averaging period in days, can be in [1, 7, 30] currently
-m NMONTHS_BACK, --nmonths_back NMONTHS_BACK
The number of months to look back, default 36
Relies on `update_OISST.py --domain NZ` to be run first
usage: OISST_realtime_Ninos_indices.py [-h] [-d DOMAIN] [-i IPATH] [-c CLIM_PATH] [-s SHAPES_PATH] [-f FIG_PATH] [-o CSV_PATH] [-n NDAYS_AGG] [-m NMONTHS_BACK]
Plot the time-series of OISST V2 SST anomalies for the Ninos regions
optional arguments:
-h, --help show this help message and exit
-d DOMAIN, --domain DOMAIN
The domain for which to download / extract, can be in ['NZ','Ninos','IOD'], default to 'Ninos' and should not change ...
-i IPATH, --ipath IPATH
The root path where the downloaded OISST datasets are, default to '/media/nicolasf/END19101/data/OISST/daily'
-c CLIM_PATH, --clim_path CLIM_PATH
The path to the zarr files containing the climatologies, default to '/home/nicolasf/operational/OISST_indices/outputs/'
-s SHAPES_PATH, --shapes_path SHAPES_PATH
The path to the shapefiles used to delineates the 6 NZ coastal regions, default to '/home/nicolasf/operational/OISST_indices/data/shapefiles/'
-f FIG_PATH, --fig_path FIG_PATH
The path to where the figures are saved, default to '/home/nicolasf/operational/OISST_indices/figures/'
-o CSV_PATH, --csv_path CSV_PATH
The path to where the csv files containing the time-series are saved '/home/nicolasf/operational/OISST_indices/outputs/'
-n NDAYS_AGG, --ndays_agg NDAYS_AGG
The averaging period in days, can be in [1, 7, 30] currently
-m NMONTHS_BACK, --nmonths_back NMONTHS_BACK
The number of months to look back, default 36
Relies on `update_OISST.py --domain Ninos` to be run first
In the notebooks directory are some notebooks mainly used to calculate the climatologies, which should only be needed to be run if calculating climatologies for another domain or another period. The main one if interest is calculate_OISST_climatologies.ipynb, it is intended to be run using papermill, but will be converted to a Python script soon.
calculate_OISST_climatologies.ipynb calculates the climatological values for a particular domain, i.e. calculates average, std, and quantiles [0.1, 0.25, 0.5, 0.75, 0.9] for a given climatology period (currently 1991 - 2020). Parameters are:
- `domain` (str): The domain used by the function `get_domain`, currently can be ['NZ', 'Ninos', 'IOD']
- `ndays` (int): The aggregation period (i.e. 1, 7 or 30 days)
- `roll` (int): The buffer (in days) around the day of the year for the calculation of the climatologies, currently set to 15, i.e. 7 days each side of the target day of the year.
- `climatology` (list): The climatological period, currently `[1991, 2020]`
- `quantiles` (list): The list of climatological quantiles to calculate, currently `[0.1, 0.25, 0.5, 0.75, 0.9]`
- `ipath` (str): The path where to find the OISST archive (`domain` will be added to the root path)
- `opath` (str): The path where the climatologies will be saved (in zarr format), `domain` will be added to the root path.
Below are examples of the maps generated
The map below shows the geometries used for the definition of the 6 NZ coastal regions (["NNI", "WNI", "ENI", "NSI", "WSI", "ESI"])
and the following figure shows an example of the time-series generated
